3IRT	Hydrolase, Ligase	date	Aug 24, 2009
title	Crystal Structure Of The I93m Mutant Of Ubiquitin Carboxy-Te Hydrolase L1
authors	C.W.Davies, T.K.Maiti, C.Das
compound		source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase Isozyme L1 Chain: A, B Synonym: Uch-L1, Ubiquitin Thioesterase L1, Neuron Cytoplas Protein 9.5, Pgp 9.5, Pgp9.5; Ec: 3.4.19.12, 6.-.-.- Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pgp9.5, Uchl1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Rosetta Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex-6p-1
symmetry	Space Group: P 4 21 2	R_factor 0.211 R_Free 0.254
crystal cell	length a length b length c angle alpha angle beta angle gamma 109.938 109.938 79.040 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	CL	enzyme	Hydrolase E.C.3.4.19.12 BRENDA
Gene Ontology	Chain Function Process Component A, B cysteine-type endopeptidase ... ubiquitin thiolesterase acti... protein binding peptidase activity cysteine-type peptidase acti... omega peptidase activity hydrolase activity ligase activity alpha-2A adrenergic receptor... ubiquitin binding proteolysis ubiquitin-dependent protein ... response to stress axonogenesis axon target recognition adult walking behavior cell death cell proliferation protein deubiquitination sensory perception of pain axon transport of mitochondr... eating behavior negative regulation of MAP k... muscle fiber development neuromuscular process nucleus nucleolus cytoplasm endoplasmic reticulum endoplasmic reticulum membra... cytosol plasma membrane membrane axon neuronal cell body
Primary reference	Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation., Boudreaux DA, Maiti TK, Davies CW, Das C, Proc Natl Acad Sci U S A. 2010 May 18;107(20):9117-22. Epub 2010 May 3. PMID:20439756

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk] Biological Unit Coordinates (3irt.pdb1.gz) 37 Kb Biological Unit Coordinates (3irt.pdb2.gz) 37 Kb LPC: Ligand-Protein Contacts for 3IRT CSU: Contacts of Structural Units for 3IRT Structure Factors (90 Kb) Retrieve 3IRT in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3IRT from S2C, [Save to disk] Re-refined 3irt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3IRT in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3IRT

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 3IRT, from MSDmotif at EBI Fold representative 3irt from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3irt_A] [3irt_B] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3IRT with the sequences similar proteins can be viewed for 3IRT's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.

Other resources with information on 3IRT

Community annotation for 3IRT at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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